[English] 日本語
![](img/lk-miru.gif)
- PDB-6lsa: Complex structure of bovine herpesvirus 1 glycoprotein D and bovi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6lsa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 IgV | |||||||||
![]() |
| |||||||||
![]() | ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. ...Yue, D. / Chen, Z.J. / Yang, F.L. / Ye, F. / Lin, S. / Cheng, Y.W. / Wang, J.C. / Chen, Z.M. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z.L. / You, Y. / Sun, H.L. / Wen, A. / Wang, L.L. / Zheng, Y. / Cao, Y. / Li, Y.H. / Lu, G.W. | |||||||||
![]() | ![]() Title: Crystal structure of bovine herpesvirus 1 glycoprotein D bound to nectin-1 reveals the basis for its low-affinity binding to the receptor. Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / ...Authors: Yue, D. / Chen, Z. / Yang, F. / Ye, F. / Lin, S. / He, B. / Cheng, Y. / Wang, J. / Chen, Z. / Lin, X. / Yang, J. / Chen, H. / Zhang, Z. / You, Y. / Sun, H. / Wen, A. / Wang, L. / Zheng, Y. / Cao, Y. / Li, Y. / Lu, G. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 306.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 246.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6ls9C ![]() 5x5wS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 12100.761 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: F1MQJ3 #2: Protein | Mass: 34871.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_ ...Gene: US6, gD, AAADCAAH_00066, BLEONNCJ_00068, BLPDLEPH_00067, DCJDKEDG_00068, DILPLKIK_00066, DJCKHMNK_00067, HMKIDIGP_00066, LALCDEHK_00068, NBBNDGNH_00066, NCKHNGOI_00066, NFOBEAPH_00067, OCMKPLLD_00067, OHMFJBFK_00067 Production host: ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() Source method: isolated from a genetically manipulated source #4: Sugar | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % |
---|---|
Crystal grow![]() | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Sodium HEPES, 15% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. obs: 58498 / % possible obs: 98.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.783 / Num. unique obs: 5751 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5X5W Resolution: 2.204→45.196 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.38
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 163.66 Å2 / Biso mean: 61.8638 Å2 / Biso min: 27.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.204→45.196 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -41.252 Å / Origin y: -31.543 Å / Origin z: 30.269 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|